Update FAQ.md

docs/FAQ.md

@@ -38,12 +38,14 @@ Yes you can! By means of a [custom config file](./usage.md#further-customization
 
 9. **How fast is varVAMP?**
 
-varVAMP is pretty fast given the complexity of the problem. Running time is dependent on the alignment length, number of sequences and the running mode. While the TILED is rather slow, qPCR and SINGLE can be faster. An alignment with a few hundred sequences and with a genome size of 10 kb will likely run in under a minute for the TILED mode. For large e.g. DNA viruses (200 kb) it takes considerably longer, but should still finish in minutes. Running time optimizations are planned.
+varVAMP is pretty fast given the complexity of the problem. Running time is dependent on the alignment length, number of sequences and the running mode. While the TILED is rather slow, qPCR and SINGLE can be faster. An alignment with a few hundred sequences and with a genome size of 10 kb will likely run in under a minute for the TILED mode. For large e.g. DNA viruses (200 kb) it takes considerably longer, but should still finish in minutes.
 
 10. **Can I contribute?**
 
 Yes, please. Give feedback to code or settings or also if you have successfully used this to design primers that make your life easier in the lab!
 
+11. **Do I have to adapt the bed file if I want to trim primer sequences in my NGS analysis pipeline?"**
 
+You can try to use varVAMP's consensus sequence for mapping. However, if you want to map to a different reference, you will need to adapt the primer's start and stop positions in the bed file to your new reference sequence. You can try to use the [varVAMP helper script developed by Namuun](https://github.com/rki-mf1/update-varvamp-bed/).
 
 #### [Previous: How it works](./how_varvamp_works.md)